Mission

The mission of the research group Metabolic Systems Interactions is to gain a better understanding of the capacities and constraints that shape the behavior of the plant’s metabolic systems and their interactions. The group uses computational approaches that are centred around the analysis of large-scale metabolic networks and works closely with experimental labs at the IPK and other research institutes in Germany and abroad.

Key topics are the development of constraint-based methods to study tissue- and organ interactions, the curation and computational integration of specialized metabolism and the study of plant-environment interactions. The gained knowledge will guide metabolic engineering strategies for improved crop plant productivity and quality. 

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Projects

We are currently working on the following topics and we are continously looking for students on all levels and PostDocs to join our team:

  • Development and application of multi-organ up to whole-plant metabolic models
  • Modelling and analysis of CAM and C4 photosynthesis
  • Software development for metabolic network reconstruction and curation
  • Computational modelling of the energetics of guard cell metabolism

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Staff

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Publications

Author
Title
2022

Branco-Vieira M, Lopes M P C, Caetano N S:

Algae-based bioenergy production aligns with the Paris agreement goals as a carbon mitigation technology. Energy Reports 8 (2022) 482-488. https://dx.doi.org/10.1016/j.egyr.2022.01.081

Caetano N S, Corrêa P S, de Morais Júnior W G, Mata T M, Martins A A A, Branco-Vieira M:

LCA: a tool to develop sustainable microalgal biorefineries. In: Bhatia S K, Mehariya S, Karthikeyan O P (Eds.): Algal biorefineries and the circular bioeconomy: industrial applications and future prospects. 1st. edition. Boca Raton: CRC Press (2022) ISBN 9781003195405, 341-387. https://dx.doi.org/10.1201/9781003195429

Caetano N S, Corrêa P S, de Morais Júnior W G, Oliveira G M, Martins A A A, Branco-Vieira M, Mata T M:

Microalgae for pigments and cosmetics. In: Mehariya S, Bhatia S K, Karthikeyan O P (Eds.): Algal biorefineries and the circular bioeconomy: algal products and processes. 1st. edition. Boca Raton: CRC Press (2022) ISBN 9781003195405, 133-176. https://dx.doi.org/10.1201/9781003195405

Camborda S, Weder J-N, Töpfer N:

CobraMod: A pathway-centric curation tool for constraint-based metabolic models. Bioinformatics 38 (2022) 2654–2656. https://dx.doi.org/10.1093/bioinformatics/btac119

Schönherr L:

Computational modelling of a photorespiratory bypass in C3 metabolism to establish a synthetic C4 cycle. (Bachelor Thesis) Mittweida, Hochschule Mittweida, Fakultät Angewandte Computer- und Biowissenschaften (2022) 85 pp.

Vieira T A S, Trugilho P F, Carabineiro S A C, Zanuncio A J V, Carvalho A G, da Silva L F, Branco-Vieira M, da Silva C M S, Carneiro A d C O:

Production of high-quality forest wood biomass using artificial intelligence to control thermal modification. Biomass Convers. Bioref. (2022) Epub ahead of print. https://dx.doi.org/10.1007/s13399-022-02666-z

2021

Sahu A, Blätke M-A, Szymański J J, Töpfer N:

Advances in flux balance analysis by integrating machine learning and mechanism-based models. Comput. Struct. Biotechnol. J. 19 (2021) 4626-4640. https://doi.org/10.1016/j.csbj.2021.08.004

Töpfer N:

Environment-coupled models of leaf metabolism. Biochem. Soc. Trans. 49 (2021) 119–129. https://dx.doi.org/10.1042/BST20200059

2020

Seidel J:

Implementation and application of computational approaches to integrate generegulatory and metabolic networks. (Bachelor Thesis) Mittweida, Hochschule Mittweida, Fakultät Angewandte Computer- und Biowissenschaften (2020)

Töpfer N, Braam T, Shameer S, Ratcliffe R G, Sweetlove L J:

Alternative Crassulacean acid metabolism modes provide environment-specific water-saving benefits in a leaf metabolic model. Plant Cell 32 (2020) 3689-3705. https://dx.doi.org/10.1105/tpc.20.00132

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